IMAP-PART 08

Exploratory Analysis of 16S-Based Microbial Profiles

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

Deep exploration of microbial profiles

…BRIEF INTRO IN PROGRESS…

Snakemake workflow for exploratory data analysis

A tentative snakemake workflow that defines data exploration rules in a DAG (directed acyclic graph) format. A detailed interactive snakemake HTML report is available here. Use a wider screen to get a better interactive snakemake report.

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using MOTHUR and Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 and Snakemake workflows	In-progress
IMAP-PART 07	Processing Output from 16S-Based microbiome bioinformatics pipelines	In-progress
IMAP-PART 08	Exploratory Analysis of 16S-Based Microbiome Processed Data	In-progress
IMAP-PART 09	Visualization of Microbiome Data with the integration of Snakemake Workflows	In-progress
IMAP-PART XX	Predictive Modeling of Microbiome Data Using Machine Learning Techniques	In-progress
IMAP-SUMMARY	Summary of snakemake workflows for microbiome data analysis	In-progress

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   └── config.yml
├── css
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature_table.qza
│   ├── features.csv
│   ├── metadata.csv
│   ├── processed_data.rda
│   ├── processed_objects.rda
│   ├── rooted_tree.qza
│   ├── sample_metadata.tsv
│   ├── shannon.csv
│   ├── shannon_vector.qza
│   ├── taxonomy.csv
│   ├── taxonomy.qza
│   └── unweighted_unifrac_pcoa.qza
├── figures
│   ├── q2r_barplot.png
│   ├── q2r_barplot.svg
│   ├── q2r_heatmap.png
│   ├── q2r_heatmap.svg
│   ├── q2r_jitterplot.png
│   ├── q2r_jitterplot.svg
│   ├── q2r_lineplot.png
│   ├── q2r_lineplot.svg
│   ├── q2r_pcoa.png
│   └── q2r_pcoa.svg
├── images
│   ├── bkgd.png
│   ├── coders.png
│   ├── ml.png
│   ├── smkreport
│   │   └── screenshot.png
│   └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   ├── packages.bib
│   └── references.bib
├── report.html
├── results
│   └── project_tree.txt
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   └── environment.yml
    ├── report
    │   ├── barplot.rst
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmap.rst
    │   ├── jitterplot.rst
    │   ├── lineplot.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoa.rst
    │   ├── scatter.rst
    │   ├── venndiagram.rst
    │   ├── volcano.rst
    │   └── workflow.rst
    ├── rules
    │   ├── import_demo_data.smk
    │   ├── render_index.smk
    │   ├── rmd_report.smk
    │   ├── rules_dag.smk
    │   ├── visual_types.smk
    │   └── visuals.smk
    └── scripts
        ├── README.md
        ├── alpha.R
        ├── barplot.R
        ├── build_bs4_book.bash
        ├── common.R
        ├── custom_theme.R
        ├── heatmap.R
        ├── import_demo_data.R
        ├── jitterplot.R
        ├── lefse.R
        ├── lineplot.R
        ├── pcoa.R
        ├── qiime2R.R
        ├── qiime2csv.R
        ├── rarefy.R
        ├── read_matrix.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        ├── tree.sh
        └── volcanoplot.R

14 directories, 84 files

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on May 08, 2023.
Github_Repo: https://github.com/tmbuza/imap-exploratory-analysis.
Repo compiled and maintained by: Teresia Mrema-Buza.